Removing duplicate bones
If your bones are named properly and uniquely, you can filter them by Select Pattern:


Go to 3D View menu, Select > Select Pattern..., then type '*.001', press Enter, then delete them all.




Or you can target them by Outliner:


Select the Armature object, switch to Edit Mode, go to Outliner, set Type to Active, then search .001 (the naming suffix to each duplicate and automatically given by Blender). Then B to select all bones, then go to 3D View, press X, choose Delete Bones.




If the methods above don't work well in your case, you can try Select Similar feature to select them quickly:


First, select the root bone, then press Shift G, choose Children, then delete them all. (For those with no children, usually you have to select them manually)